1. SBML Viewer Laurent Francioli

2. Introduction SBML Viewer is… A java application belonging to the bio-chemical modelling tools framework –Provides graphical representation of the bio-chemical models –Prepares these models for simulation –Regroups all the features of the framework under a GUI A semester project done in the Laboratory for computer Communications and Applications at the Swiss Institute of Technology

3. Why SBML Viewer? Provides global vision and understanding of the bio-chemical models Easy visual checking of models structure Graphing of a widely used language in bioinformatics: SBML Graphical knowledge sharing platform Provides tools to prepare a model for simulation

4. Graphical Representation of biological Networks Challenging due to their complexity and their high connectivity Shall be: Easy to read Precise Complete Unambiguous

5. From SBML to a Graph A graph needs: –The structure that describes the entities and their connectivity –The layout of the graph that describes the positioning of the entities on the screen SBML only contains the structure of the biological network Current State-of-the-art –Doesn’t provide automatic layout algorithms –Redundancy of structural information

6. Automatic Layout A NP Complex problem Several algorithms present in SBML Viewer These algorithms are not tailored to biological networks –They give a good starting point to the desired layout –They always require some manual work afterwards

7. A Simple Example

8. Simulated Annealing Layout

9. GEM Layout

10. Sugiyama Layout

11. Preparation of a model for simulation A simulation needs: –A model –An initial state of the system Our framework, through TSed, provides the model SBML Viewer provides dialogs to easily setup its initial state by setting the initial amount of each species

12. Conclusion SBML Viewer today: –Provides a link between a model and its simulation –Semi-automatically layouts graphs from a model SBML Viewer tomorrow: –Enhanced automatic layout using tailored algorithms –Model creation and edition tools –Automated layered graph representation for large biological networks

13. ? Questions ?